Archive for August, 2013

Two Open Tree participants, Romina Gazis and David Hibbett, recently attended the annual meeting of the Mycological Society of America in Austin, Texas. Romina gave a presentation about the Open Tree of Life Project, which gave us a chance to hear some thoughts from our community. Questions (paraphrased) included the following:

“When the synthetic tree is available, will we be able to filter on a node-by-node basis, or just tree-by-tree? For example, will we be able to identify the strongly supported nodes in individual trees and then constrain the synthetic tree to include those nodes, but not other, weakly supported nodes?”

Capturing information about individual branches, such as support values and branch lengths, is difficult, and in some cases impossible, because the trees were deposited without such information included. It is possible to make decisions about priority on a node-by-node basis, but this requires decision-making by the individual performing the synthesis.

“Can this synthetic view of the tree be used to guide genome sampling priorities?”

Absolutely! In fact, the ongoing 1000 Fungal Genomes Project is already using taxonomy to guide sampling. Open Tree will be able to help in this effort by providing a comprehensive view of phylogenetic diversity of Fungi that will help identify clades that are poorly sampled. We will also be able to prioritize genome-based studies during synthesis, which should allow us to create trees based on a very robust backbone.

Numerous talks and posters at MSA concerned fungal phylogenetics and taxonomy. So much progress is being made! For example, there were presentations on systematics of chytrids, downy midlews, rusts, earth tongues, lichens, mushrooms, and many more. At the same time, in the course of developing the first synthetic trees for this project, it has become abundantly clear that the major centralized taxonomic resources, like Global Biodiversity Information Facility (GBIF) and National Center for Biotechnology Information (NCBI) have a hard time capturing phylogenetic knowledge. To be fair, it is unreasonable to think that any single organization can keep track of all the progress in taxon discovery and phylogenetic inference across the entire tree of life. Sitting in the audience at MSA, I wondered how long it would take for the trees being projected on-screen to be reflected in the taxonomy presented by organizations like GBIF or NCBI (or EoL , CoL, etc). Perhaps a new, community-based approach is needed for building a taxonomic commons?